{"id":4318,"date":"2018-09-18T12:16:25","date_gmt":"2018-09-18T11:16:25","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=4318"},"modified":"2018-10-24T15:55:34","modified_gmt":"2018-10-24T14:55:34","slug":"so-you-are-interested-in-compound-selectivity-and-machine-learning-papers","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2018\/09\/so-you-are-interested-in-compound-selectivity-and-machine-learning-papers\/","title":{"rendered":"So, you are interested in compound selectivity and machine learning papers?"},"content":{"rendered":"<p>At the last OPIG meeting, I gave a talk about compound selectivity and machine learning approaching to predict whether a compound might be selective. As promised, I hereby provide a list publications I would hand to a beginner in the field of compound selectivity and machine learning.&nbsp;<!--more--><\/p>\n<p><b>Concept of <\/b><b>&nbsp;compound selectivity (based on structural or ligand features)? Read these publication!<\/b><\/p>\n<ul>\n<li>Haupt, V. J., Daminelli, S. &amp; Schroeder, M. Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLoS One 8, 1\u201315 (2013).<\/li>\n<li>Sturm, N., Desaphy, J., Quinn, R. J., Rognan, D. &amp; Kellenberger, E. Structural insights into the molecular basis of the ligand promiscuity. J. Chem. Inf. Model. 52, 2410\u20132421 (2012).<\/li>\n<li>Hu, Y. &amp; Bajorath, J. Compound promiscuity: What can we learn from current data? Drug Discov. Today 18, 644\u2013650 (2013).<\/li>\n<li>Baell, J. &amp; Walters, M. A. Chemistry: Chemical con artists foil drug discovery. Nature 513, 481\u2013483 (2014).<\/li>\n<\/ul>\n<p><strong>More about &#8216;Chemical Probes&#8217; or &#8216;Tool Compounds&#8217;, compounds which are highly selective towards a specific target? Read these publications!<\/strong><\/p>\n<ul>\n<li>Arrowsmith, C. H. et al. The promise and peril of chemical probes. Nat. Chem. Biol. 11, 536\u2013541 (2015).<\/li>\n<li><span style=\"font-size: 1rem;\">Wang, Y. et al. Evidence-Based and Quantitative Prioritization of Tool Compounds in Phenotypic Drug Discovery. Cell Chem. Biol. 23, 862\u2013874 (2016).<\/span><\/li>\n<li><span style=\"font-size: 1rem;\">Butler, K. V, Macdonald, I. A., Hathaway, N. A. &amp; Jin, J. Report and Application of a Tool Compound Data Set. J. Chem. Inf. Model 57, 2699\u22122706 (2017).<\/span><\/li>\n<\/ul>\n<p><strong>Machine Learning to determine compound selectivity? Read these publications!<\/strong><\/p>\n<ul>\n<li>Sorgenfrei, F. A., Fulle, S. &amp; Merget, B. Kinome-Wide Profiling Prediction of Small Molecules. ChemMedChem 1\u20136 (2017).<\/li>\n<li>Giblin, K., Hughes, S., Boyd, H., Hansson, P. &amp; Bender, A. Prospectively Validated Proteochemometric Models for the Prediction of Small Molecule Binding to Bromodomain Proteins. J. Chem. Inf. Model. XXXX, XXX, XXX-XXX acs.jcim.8b00400 (2018).<\/li>\n<li>Subramanian, V., Prusis, P., Pietil\u00e4, L. O., Xhaard, H. &amp; Wohlfahrt, G. Visually interpretable models of kinase selectivity related features derived from field-based proteochemometrics. <i>J. Chem. Inf. Model.<\/i> <b>53,<\/b> 3021\u20133030 (2013).<\/li>\n<\/ul>\n<p><strong>Interested in more machine learning as an extension to the publications above? These publications might be a good starting point&#8230;<\/strong><\/p>\n<ul>\n<li>Cort\u00e9s-Ciriano, I. et al. Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects. Med. Chem. Commun. 6, 24\u201350 (2015).<\/li>\n<li>Krstajic, D., Buturovic, L. J., Leahy, D. E. &amp; Thomas, S. Cross-validation pitfalls when selecting and assessing regression and classification models. J. Cheminform. 6, 1\u201315 (2014).<\/li>\n<li>Sun, J. et al. Applying Mondrian Cross-Conformal Prediction to Estimate Prediction Confidence on Large Imbalanced Bioactivity Data Sets. J. Chem. Inf. Model. 57, 1591\u20131598 (2017).<\/li>\n<\/ul>\n<p>best,<br \/>\nAnne<\/p>\n","protected":false},"excerpt":{"rendered":"<p>At the last OPIG meeting, I gave a talk about compound selectivity and machine learning approaching to predict whether a compound might be selective. As promised, I hereby provide a list publications I would hand to a beginner in the field of compound selectivity and machine learning.&nbsp;<\/p>\n","protected":false},"author":44,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[187,189,201,9,15],"tags":[203],"ppma_author":[495],"class_list":["post-4318","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-machine-learning","category-small-molecules","category-talks","category-technical","tag-publication"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":495,"user_id":44,"is_guest":0,"slug":"anne","display_name":"Anne Nierobisch","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/ca4e669549272020b68503a44f391f6376a9859e3975265369e719141b4d1d19?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4318","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/44"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=4318"}],"version-history":[{"count":5,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4318\/revisions"}],"predecessor-version":[{"id":4390,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4318\/revisions\/4390"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=4318"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=4318"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=4318"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=4318"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}